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Virome of red sea brine pools and other hydrothermal vents
The central rift of the Red Sea has 25 brine pools that vary in their physical and geochemical characteristics, three of which, Atlantis II (ATIID), Discovery Deep (DD) and Kebrit Deep (KD), have high salinity, temperature and metal content. Previous studies reported bacterial and archaeal inhabitan...
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2017
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| _version_ | 1867613411574022144 |
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| access_status_str | Open Access |
| author | Aziz, Sherry Kamal Berty |
| author_browse | Aziz, Sherry Kamal Berty |
| author_facet | Aziz, Sherry Kamal Berty |
| author_sort | Aziz, Sherry Kamal Berty |
| collection | Thesis |
| dc_rights_str_mv | The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. |
| description | The central rift of the Red Sea has 25 brine pools that vary in their physical and geochemical characteristics, three of which, Atlantis II (ATIID), Discovery Deep (DD) and Kebrit Deep (KD), have high salinity, temperature and metal content. Previous studies reported bacterial and archaeal inhabitants in these brine pools, but few studies addressed the viral communities. Therefore, sediment cores and water samples were collected from ATIID, DD, KD brine pools in addition to a neighboring two brine-influenced sites. Shotgun DNA pyrosequencing was performed to all samples. Sediment-specific reads were generated and annotated. The phylogenetic and biochemical uniqueness of the deepest ATIID brine pool sediments was clearly reported with unique viral signature for the deepest two layers. Bacteria dominate the deepest ATIID sediments sections whereas viruses are more prevalent in other sediment sections. Water samples were also collected and analyzed for their viral community. Water and sediment samples were analyzed using different approaches. The traditional method of analysis was used in addition to another approach called Genome relative Abundance and Average Size (GAAS) approach which showed that there is an enormous data that was overlooked using the classical method. GAAS estimates both viral abundance and the average genome size for each section to overcome the disadvantage of sampling bias during viral analysis. Different sections showed different viral communities and different average genome sizes based on different stressors. Shannon diversity index, richness and evenness were calculated for each section to obtain accurate estimates of viral inhabitants. Our results showed that there is direct relationship between viral diversity and average genome sizes. Interestingly, prophages and gene transfer agents (GTAs) were also identified in the analysis of the Red Sea brine pools such as Rhodobacter phage. It was linked to horizontal gene transfer, viral diversity and evolution. Other hydrothermal vents were also analyzed for their viral communities and compared to the Red Sea brine pools. The highest Shannon diversity index was estimated in the Red Sea hydrothermal vent which renders the Red Sea environments more unique and distinct from other hydrothermal vents. |
| format | Thesis |
| id | oai:fount.aucegypt.edu:etds-1641 |
| institution | American University in Cairo (Egypt) |
| last_indexed | 2026-06-10T12:35:43.583Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from AUC Knowledge Fountain — bepress |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | AUC Knowledge Fountain |
| publisherStr | AUC Knowledge Fountain |
| record_format | dspace |
| source_str | AUC Knowledge Fountain — bepress |
| spelling | oai:fount.aucegypt.edu:etds-1641 Virome of red sea brine pools and other hydrothermal vents Aziz, Sherry Kamal Berty The central rift of the Red Sea has 25 brine pools that vary in their physical and geochemical characteristics, three of which, Atlantis II (ATIID), Discovery Deep (DD) and Kebrit Deep (KD), have high salinity, temperature and metal content. Previous studies reported bacterial and archaeal inhabitants in these brine pools, but few studies addressed the viral communities. Therefore, sediment cores and water samples were collected from ATIID, DD, KD brine pools in addition to a neighboring two brine-influenced sites. Shotgun DNA pyrosequencing was performed to all samples. Sediment-specific reads were generated and annotated. The phylogenetic and biochemical uniqueness of the deepest ATIID brine pool sediments was clearly reported with unique viral signature for the deepest two layers. Bacteria dominate the deepest ATIID sediments sections whereas viruses are more prevalent in other sediment sections. Water samples were also collected and analyzed for their viral community. Water and sediment samples were analyzed using different approaches. The traditional method of analysis was used in addition to another approach called Genome relative Abundance and Average Size (GAAS) approach which showed that there is an enormous data that was overlooked using the classical method. GAAS estimates both viral abundance and the average genome size for each section to overcome the disadvantage of sampling bias during viral analysis. Different sections showed different viral communities and different average genome sizes based on different stressors. Shannon diversity index, richness and evenness were calculated for each section to obtain accurate estimates of viral inhabitants. Our results showed that there is direct relationship between viral diversity and average genome sizes. Interestingly, prophages and gene transfer agents (GTAs) were also identified in the analysis of the Red Sea brine pools such as Rhodobacter phage. It was linked to horizontal gene transfer, viral diversity and evolution. Other hydrothermal vents were also analyzed for their viral communities and compared to the Red Sea brine pools. The highest Shannon diversity index was estimated in the Red Sea hydrothermal vent which renders the Red Sea environments more unique and distinct from other hydrothermal vents. 2017-02-01T08:00:00Z thesis application/pdf https://fount.aucegypt.edu/etds/642 https://fount.aucegypt.edu/context/etds/article/1641/viewcontent/Virome_20of_20Red_20Sea_20Brine_20Pools_20and_20Other_20Hydrothermal_20Vents.pdf The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. Theses and Dissertations AUC Knowledge Fountain virome red sea |
| spellingShingle | virome red sea Aziz, Sherry Kamal Berty Virome of red sea brine pools and other hydrothermal vents |
| title | Virome of red sea brine pools and other hydrothermal vents |
| title_full | Virome of red sea brine pools and other hydrothermal vents |
| title_fullStr | Virome of red sea brine pools and other hydrothermal vents |
| title_full_unstemmed | Virome of red sea brine pools and other hydrothermal vents |
| title_short | Virome of red sea brine pools and other hydrothermal vents |
| title_sort | virome of red sea brine pools and other hydrothermal vents |
| topic | virome red sea |
| url | https://fount.aucegypt.edu/etds/642 https://fount.aucegypt.edu/context/etds/article/1641/viewcontent/Virome_20of_20Red_20Sea_20Brine_20Pools_20and_20Other_20Hydrothermal_20Vents.pdf |
| work_keys_str_mv | AT azizsherrykamalberty viromeofredseabrinepoolsandotherhydrothermalvents |